I hadn't played basketball for a long time

I take the meaning to be your first ("I played basketball two days ago; I hadn't played for a long time."). In order to mean the second, it would need to be rendered something like:

I had never played basketball for very long at a time until two days ago.

However, having said that, the original sentence would be clearer by beginning with the prepositional phrase in order to emphasize it, like this:

Until two days ago, I hadn't played basketball for [or in] a long time.